bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2022–06–05
fourteen papers selected by
Ralitsa Radostinova Madsen, University College London
  1. Non-canonical mTORC1 signaling at the lysosome.
  2. Endothelial Cell Insulin Signaling Regulates CXCR4 (C-X-C Motif Chemokine Receptor 4) and Limits Leukocyte Adhesion to Endothelium.
  3. MET∆14 promotes a ligand-dependent, AKT-driven invasive growth.
  4. Catch them if you are aware: PTEN postzygotic mosaicism in clinically suspicious patients with PTEN Hamartoma Tumour Syndrome and literature review.
  5. Integrated DNA and RNA Sequencing Reveals Drivers of Endocrine Resistance in Estrogen Receptor-Positive Breast Cancer.
  6. Nuclear Vav3 is required for polycomb repression complex-1 activity in B-cell lymphoblastic leukemogenesis.
  7. The role of the PI3K/AKT signalling pathway in the corneal epithelium: recent updates.
  8. mTORC1-independent translation control in mammalian cells by methionine adenosyltransferase 2A and S-adenosylmethionine.
  9. Cancer-cell-secreted extracellular vesicles suppress insulin secretion through miR-122 to impair systemic glucose homeostasis and contribute to tumour growth.
  10. Lipid balance must be just right to prevent development of severe liver damage.
  11. Endothelial Cells Induced Progenitors Into Brown Fat to Reduce Atherosclerosis.
  12. Fast and highly sensitive full-length single-cell RNA sequencing using FLASH-seq.
  13. Scalable single-cell RNA sequencing from full transcripts with Smart-seq3xpress.
  14. PCGA: a comprehensive web server for phenotype-cell-gene association analysis.
  1. Trends Cell Biol. 2022 May 30. pii: S0962-8924(22)00117-9. [Epub ahead of print]
    Non-canonical mTORC1 signaling at the lysosome.
    Gennaro Napolitano, Chiara Di Malta, Andrea Ballabio.
      The mechanistic target of rapamycin complex 1 (mTORC1) signaling hub integrates multiple environmental cues to modulate cell growth and metabolism. Over the past decade considerable knowledge has been gained on the mechanisms modulating mTORC1 lysosomal recruitment and activation. However, whether and how mTORC1 is able to elicit selective responses to diverse signals has remained elusive until recently. We discuss emerging evidence for a 'non-canonical' mTORC1 signaling pathway that controls the function of microphthalmia/transcription factor E (MiT-TFE) transcription factors, key regulators of cell metabolism. This signaling pathway is mediated by a specific mechanism of substrate recruitment, and responds to stimuli that appear to converge on the lysosomal surface. We discuss the relevance of this pathway in physiological and disease conditions.
    Keywords:  FLCN; Rag GTPases; TFEB; lysosome; mTORC1
    DOI:  https://doi.org/10.1016/j.tcb.2022.04.012
  2. Arterioscler Thromb Vasc Biol. 2022 Jun 02. 101161101161ATVBAHA122317476
    Endothelial Cell Insulin Signaling Regulates CXCR4 (C-X-C Motif Chemokine Receptor 4) and Limits Leukocyte Adhesion to Endothelium.
    Thomas Rathjen, Britta Kunkemoeller, Carly T Cederquist, Xuanchun Wang, Sam M Lockhart, James C Patti, Hanni Willenbrock, Grith Skytte Olsen, Gro Klitgaard Povlsen, Hans Christian Beck, Lars Melholt Rasmussen, Qian Li, Kyoungmin Park, George L King, Christian Rask-Madsen.
       BACKGROUND: An activated, proinflammatory endothelium is a key feature in the development of complications of obesity and type 2 diabetes and can be caused by insulin resistance in endothelial cells.
    METHODS: We analyzed primary human endothelial cells by RNA sequencing to discover novel insulin-regulated genes and used endothelial cell culture and animal models to characterize signaling through CXCR4 (C-X-C motif chemokine receptor 4) in endothelial cells.
    RESULTS: CXCR4 was one of the genes most potently regulated by insulin, and this was mediated by PI3K (phosphatidylinositol 3-kinase), likely through FoxO1, which bound to the CXCR4 promoter. CXCR4 mRNA in CD31+ cells was 77% higher in mice with diet-induced obesity compared with lean controls and 37% higher in db/db mice than db/+ controls, consistent with upregulation of CXCR4 in endothelial cell insulin resistance. SDF-1 (stromal cell-derived factor-1)-the ligand for CXCR4-increased leukocyte adhesion to cultured endothelial cells. This effect was lost after deletion of CXCR4 by gene editing while 80% of the increase was prevented by treatment of endothelial cells with insulin. In vivo microscopy of mesenteric venules showed an increase in leukocyte rolling after intravenous injection of SDF-1, but most of this response was prevented in transgenic mice with endothelial overexpression of IRS-1 (insulin receptor substrate-1).
    CONCLUSIONS: Endothelial cell insulin signaling limits leukocyte/endothelial cell interaction induced by SDF-1 through downregulation of CXCR4. Improving insulin signaling in endothelial cells or inhibiting endothelial CXCR4 may reduce immune cell recruitment to the vascular wall or tissue parenchyma in insulin resistance and thereby help prevent several vascular complications.
    Keywords:  diabetes; endothelial cells; insulin receptor substrate proteins; insulin resistance; mice
    DOI:  https://doi.org/10.1161/ATVBAHA.122.317476
  3. Life Sci Alliance. 2022 Oct;pii: e202201409. [Epub ahead of print]5(10):
    MET∆14 promotes a ligand-dependent, AKT-driven invasive growth.
    Marina Cerqua, Orsola Botti, Maddalena Arigoni, Noemi Gioelli, Guido Serini, Raffaele Calogero, Carla Boccaccio, Paolo M Comoglio, Dogus M Altintas.
      MET is an oncogene encoding the tyrosine kinase receptor for hepatocyte growth factor (HGF). Upon ligand binding, MET activates multiple signal transducers, including PI3K/AKT, STAT3, and MAPK. When mutated or amplified, MET becomes a "driver" for the onset and progression of cancer. The most frequent mutations in the MET gene affect the splicing sites of exon 14, leading to the deletion of the receptor's juxtamembrane domain (MET∆14). It is currently believed that, as in gene amplification, MET∆14 kinase is constitutively active. Our analysis of MET in carcinoma cell lines showed that MET∆14 strictly depends on HGF for kinase activation. Compared with wt MET, ∆14 is sensitive to lower HGF concentrations, with more sustained kinase response. Using three different models, we have demonstrated that MET∆14 activation leads to robust phosphorylation of AKT, leading to a distinctive transcriptomic signature. Functional studies revealed that ∆14 activation is predominantly responsible for enhanced protection from apoptosis and cellular migration. Thus, the unique HGF-dependent ∆14 oncogenic activity suggests consideration of HGF in the tumour microenvironment to select patients for clinical trials.
    DOI:  https://doi.org/10.26508/lsa.202201409
  4. Eur J Med Genet. 2022 May 28. pii: S1769-7212(22)00114-8. [Epub ahead of print] 104533
    Catch them if you are aware: PTEN postzygotic mosaicism in clinically suspicious patients with PTEN Hamartoma Tumour Syndrome and literature review.
    Linda A J Hendricks, Janneke Schuurs-Hoeijmakers, Isabel Spier, M L Haadsma, Astrid Eijkelenboom, Kirsten Cremer, Arjen R Mensenkamp, Stefan Aretz, Janet R Vos, Nicoline Hoogerbrugge.
      PTEN germline variants cause PTEN Hamartoma Tumour Syndrome (PHTS). Of individuals fulfilling diagnostic criteria, 41-88% test negative for PTEN germline variants, while mosaicism could be an explanation. Here we describe two individuals with PTEN mosaicism. First, a 21-year-old female presented with macrocephaly and a venous malformation. Next generation sequencing analysis on her venous malformation identified the mosaic pathogenic PTEN variant c.493-2 A > G (23%). This variant was initially missed in blood due to low frequency (<1%), but detected in buccal swab (21%). Second, a 13-year-old male presented with macrocephaly, language developmental delay, behavioral problems, and an acral hyperkeratotic papule. Targeted PTEN analysis identified the mosaic pathogenic variant c.284C > T (11%) in blood, which was confirmed via buccal swab. These two cases suggest that PTEN mosaicism might be more common than currently reported. PTEN mosaicism awareness is important to enable diagnosis, which facilitates timely inclusion in cancer surveillance-programs improving prognosis and life expectancy.
    Keywords:  Cowden syndrome; Hamartoma syndrome; Mosaicism; Multiple; PTEN
    DOI:  https://doi.org/10.1016/j.ejmg.2022.104533
  5. Clin Cancer Res. 2022 Jun 02. pii: clincanres.3189.2021-9-2 12:04:46.737. [Epub ahead of print]
    Integrated DNA and RNA Sequencing Reveals Drivers of Endocrine Resistance in Estrogen Receptor-Positive Breast Cancer.
    Youli Xia, Xiaping He, Lorna Renshaw, Carlos Martinez-Perez, Charlene Kay, Mark Gray, James Meehan, Joel S Parker, Charles M Perou, Lisa A Carey, J Michael Dixon, Arran Turnbull.
       PURPOSE: Endocrine therapy resistance (ETR) remains the greatest challenge in treating patients with hormone receptor-positive breast cancer. We set out to identify molecular mechanisms underlying ETR through in-depth genomic analysis of breast tumors.
    EXPERIMENTAL DESIGN: We collected pre-treatment and sequential on-treatment tumor samples from 35 patients with estrogen receptor-positive breast cancer treated with neoadjuvant then adjuvant ET; 3 had intrinsic resistance, 19 acquired resistance, and 13 remained sensitive. Response was determined by changes in tumor volume neoadjuvantly and by monitoring for adjuvant recurrence. Twelve patients received 2 or more lines of ET, with subsequent treatment lines being initiated at the time of development of resistance to the previous ET. DNA whole-exome sequencing and RNA-sequencing were performed on all samples, totalling 169 unique specimens. DNA mutations, copy number alterations and gene expression data were analyzed through unsupervised and supervised analyses to identify molecular features related to ETR.
    RESULTS: Mutations enriched in ETR included ESR1 and GATA3. The known ESR1 D538G variant conferring ETR was identified, as was a rarer E380Q variant that confers endocrine hypersensitivity. Resistant tumors which acquired resistance had distinct gene expression profiles compared to paired sensitive tumors, showing elevated pathways including ER, HER2, GATA3, AKT, RAS and p63 signaling. Integrated analysis in individual patients highlighted the diversity of ETR mechanisms.
    CONCLUSIONS: The mechanisms underlying ETR are multiple and characterized by diverse changes in both somatic genetic and transcriptomic profiles; to overcome resistance will require an individualized approach utilizing genomic and genetic biomarkers and drugs tailored to each patient.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-21-3189
  6. Nat Commun. 2022 Jun 01. 13(1): 3056
    Nuclear Vav3 is required for polycomb repression complex-1 activity in B-cell lymphoblastic leukemogenesis.
    R C Nayak, K H Chang, A K Singh, M Kotliar, M Desai, A M Wellendorf, M Wunderlich, J Bartram, B Mizukawa, M Cuadrado, P Dexheimer, A Barski, X R Bustelo, N N Nassar, J A Cancelas.
      Acute B-cell lymphoblastic leukemia (B-ALL) results from oligo-clonal evolution of B-cell progenitors endowed with initiating and propagating leukemia properties. The activation of both the Rac guanine nucleotide exchange factor (Rac GEF) Vav3 and Rac GTPases is required for leukemogenesis mediated by the oncogenic fusion protein BCR-ABL. Vav3 expression becomes predominantly nuclear upon expression of BCR-ABL signature. In the nucleus, Vav3 interacts with BCR-ABL, Rac, and the polycomb repression complex (PRC) proteins Bmi1, Ring1b and Ezh2. The GEF activity of Vav3 is required for the proliferation, Bmi1-dependent B-cell progenitor self-renewal, nuclear Rac activation, protein interaction with Bmi1, mono-ubiquitination of H2A(K119) (H2AK119Ub) and repression of PRC-1 (PRC1) downstream target loci, of leukemic B-cell progenitors. Vav3 deficiency results in de-repression of negative regulators of cell proliferation and repression of oncogenic transcriptional factors. Mechanistically, we show that Vav3 prevents the Phlpp2-sensitive and Akt (S473)-dependent phosphorylation of Bmi1 on the regulatory residue S314 that, in turn, promotes the transcriptional factor reprogramming of leukemic B-cell progenitors. These results highlight the importance of non-canonical nuclear Rho GTPase signaling in leukemogenesis.
    DOI:  https://doi.org/10.1038/s41467-022-30651-7
  7. Cell Death Dis. 2022 May 31. 13(5): 513
    The role of the PI3K/AKT signalling pathway in the corneal epithelium: recent updates.
    Kuangqi Chen, Yanqing Li, Xuhong Zhang, Rahim Ullah, Jianping Tong, Ye Shen.
      Phosphatidylinositol 3 kinase (PI3K)/AKT (also called protein kinase B, PKB) signalling regulates various cellular processes, such as apoptosis, cell proliferation, the cell cycle, protein synthesis, glucose metabolism, and telomere activity. Corneal epithelial cells (CECs) are the outermost cells of the cornea; they maintain good optical performance and act as a physical and immune barrier. Various growth factors, including epidermal growth factor receptor (EGFR) ligands, insulin-like growth factor 1 (IGF1), neurokinin 1 (NK-1), and insulin activate the PI3K/AKT signalling pathway by binding their receptors and promote antiapoptotic, anti-inflammatory, proliferative, and migratory functions and wound healing in the corneal epithelium (CE). Reactive oxygen species (ROS) regulate apoptosis and inflammation in CECs in a concentration-dependent manner. Extreme environments induce excess ROS accumulation, inhibit PI3K/AKT, and cause apoptosis and inflammation in CECs. However, at low or moderate levels, ROS activate PI3K/AKT signalling, inhibiting apoptosis and stimulating proliferation of healthy CECs. Diabetes-associated hyperglycaemia directly inhibit PI3K/AKT signalling by increasing ROS and endoplasmic reticulum (ER) stress levels or suppressing the expression of growth factors receptors and cause diabetic keratopathy (DK) in CECs. Similarly, hyperosmolarity and ROS accumulation suppress PI3K/AKT signalling in dry eye disease (DED). However, significant overactivation of the PI3K/AKT signalling pathway, which mediates inflammation in CECs, is observed in both infectious and noninfectious keratitis. Overall, upon activation by growth factors and NK-1, PI3K/AKT signalling promotes the proliferation, migration, and anti-apoptosis of CECs, and these processes can be regulated by ROS in a concentration-dependent manner. Moreover, PI3K/AKT signalling pathway is inhibited in CECs from individuals with DK and DED, but is overactivated by keratitis.
    DOI:  https://doi.org/10.1038/s41419-022-04963-x
  8. J Biol Chem. 2022 May 27. pii: S0021-9258(22)00525-7. [Epub ahead of print] 102084
    mTORC1-independent translation control in mammalian cells by methionine adenosyltransferase 2A and S-adenosylmethionine.
    Mahabub Alam, Hiroki Shima, Yoshitaka Matsuo, Chi Long Nguyen, Mitsuyo Matsumoto, Yusho Ishii, Nichika Sato, Takato Sugiyama, Risa Nobuta, Satoshi Hashimoto, Liang Liu, Mika K Kaneko, Yukinari Kato, Toshifumi Inada, Kazuhiko Igarashi.
      Methionine adenosyltransferase (MAT) catalyzes the synthesis of S-adenosylmethionine (SAM). As the sole methyl-donor for methylation of DNA, RNA and proteins, SAM levels affect gene expression by changing methylation patterns. Expression of MAT2A, the catalytic subunit of isozyme MAT2, is positively correlated with proliferation of cancer cells; however, how MAT2A promotes cell proliferation is largely unknown. Given that the protein synthesis is induced in proliferating cells and that RNA and protein components of translation machinery are methylated, we tested here whether MAT2 and SAM are coupled with protein synthesis. By measuring ongoing protein translation via puromycin labeling, we revealed that MAT2A depletion or chemical inhibition reduced protein synthesis in HeLa and Hepa1 cells. Furthermore, overexpression of MAT2A enhanced protein synthesis, indicating that SAM is limiting under normal culture conditions. In addition, MAT2 inhibition did not accompany reduction in mTORC1 activity, but nevertheless reduced polysome formation. Polysome-bound RNA sequencing revealed that MAT2 inhibition decreased translation efficiency of some fraction of mRNAs. MAT2A was also found to interact with the proteins involved in rRNA processing and ribosome biogenesis; depletion or inhibition of MAT2 reduced 18S rRNA processing. Finally, quantitative mass spectrometry revealed that some translation factors were dynamically methylated in response to the activity of MAT2A or availability of SAM. These observations suggest that cells possess an mTOR-independent regulatory mechanism that tunes translation in response to the levels of SAM. Such a system may acclimate cells for survival when SAM synthesis is reduced, whereas it may support proliferation when SAM is sufficient.
    Keywords:  S-adenosylmethionine; mTORC1; methionine adenosyltransferase 2A; methylation; ribosome; translation; translation factor
    DOI:  https://doi.org/10.1016/j.jbc.2022.102084
  9. Nat Cell Biol. 2022 May 30.
    Cancer-cell-secreted extracellular vesicles suppress insulin secretion through miR-122 to impair systemic glucose homeostasis and contribute to tumour growth.
    Minghui Cao, Roi Isaac, Wei Yan, Xianhui Ruan, Li Jiang, Yuhao Wan, Jessica Wang, Emily Wang, Christine Caron, Steven Neben, Denis Drygin, Donald P Pizzo, Xiwei Wu, Xuxiang Liu, Andrew R Chin, Miranda Y Fong, Ziting Gao, Kaizhu Guo, Oluwole Fadare, Richard B Schwab, Yuan Yuan, Susan E Yost, Joanne Mortimer, Wenwan Zhong, Wei Ying, Jack D Bui, Dorothy D Sears, Jerrold M Olefsky, Shizhen Emily Wang.
      Epidemiological studies demonstrate an association between breast cancer (BC) and systemic dysregulation of glucose metabolism. However, how BC influences glucose homeostasis remains unknown. We show that BC-derived extracellular vesicles (EVs) suppress pancreatic insulin secretion to impair glucose homeostasis. EV-encapsulated miR-122 targets PKM in β-cells to suppress glycolysis and ATP-dependent insulin exocytosis. Mice receiving high-miR-122 EVs or bearing BC tumours exhibit suppressed insulin secretion, enhanced endogenous glucose production, impaired glucose tolerance and fasting hyperglycaemia. These effects contribute to tumour growth and are abolished by inhibiting EV secretion or miR-122, restoring PKM in β-cells or supplementing insulin. Compared with non-cancer controls, patients with BC have higher levels of circulating EV-encapsulated miR-122 and fasting glucose concentrations but lower fasting insulin; miR-122 levels are positively associated with glucose and negatively associated with insulin. Therefore, EV-mediated impairment of whole-body glycaemic control may contribute to tumour progression and incidence of type 2 diabetes in some patients with BC.
    DOI:  https://doi.org/10.1038/s41556-022-00919-7
  10. J Clin Invest. 2022 Jun 01. pii: e160326. [Epub ahead of print]132(11):
    Lipid balance must be just right to prevent development of severe liver damage.
    Timothy F Osborne, Peter J Espenshade.
      Nonalcoholic fatty liver disease (NAFLD) is a major health concern that often associates with obesity and diabetes. Fatty liver is usually a benign condition, yet a fraction of individuals progress to severe forms of liver damage, including nonalcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC). Elevated sterol regulatory element-binding protein-driven (SREBP-driven) hepatocyte lipid synthesis is associated with NAFLD in humans and mice. In this issue of the JCI, Kawamura, Matsushita, et al. evaluated the role of SREBP-dependent lipid synthesis in the development of NAFLD, NASH, and HCC in the phosphatase and tensin homolog-knockout (PTEN-knockout) NASH model. Deletion of the gene encoding SREBP cleavage-activating protein (SCAP) from the liver resulted in decreased hepatic lipids, as expected. However, SCAP deletion accelerated progression to more severe liver damage, including NASH and HCC. This study provides a note of caution for those pursuing de novo fat biosynthesis as a therapeutic intervention in human NASH.
    DOI:  https://doi.org/10.1172/JCI160326
  11. Circ Res. 2022 Jun 01. 101161CIRCRESAHA121319582
    Endothelial Cells Induced Progenitors Into Brown Fat to Reduce Atherosclerosis.
    Kyoungmin Park, Qian Li, Matthew D Lynes, Hisashi Yokomizo, Ernesto Maddaloni, Takanori Shinjo, Ronald St-Louis, Qin Li, Sayaka Katagiri, Jialin Fu, Allen Clermont, Hyunseok Park, I-Hsien Wu, Marc Gregory Yu, Hetal Shah, Yu-Hua Tseng, George L King.
       BACKGROUND: Insulin resistance (IR) can increase atherosclerotic and cardiovascular risk by inducing endothelial dysfunction, decreasing nitric oxide (NO) production, and accelerating arterial inflammation. The aim is to determine the mechanism by which insulin action and NO production in endothelial cells can improve systemic bioenergetics and decrease atherosclerosis via differentiation of perivascular progenitor cells (PPCs) into brown adipocytes (BAT).
    METHODS: Studies used various endothelial transgenic and deletion mutant ApoE-/- mice of insulin receptors, eNOS (endothelial NO synthase) and ETB (endothelin receptor type B) receptors for assessments of atherosclerosis. Cells were isolated from perivascular fat and micro-vessels for studies on differentiation and signaling mechanisms in responses to NO, insulin, and lipokines from BAT.
    RESULTS: Enhancing insulin's actions on endothelial cells and NO production in ECIRS1 transgenic mice reduced body weight and increased systemic energy expenditure and BAT mass and activity by inducing differentiation of PPCs into beige/BAT even with high-fat diet. However, positive changes in bioenergetics, BAT differentiation from PPCs and weight loss were inhibited by N(gamma)-nitro-L-arginine methyl ester (L-NAME), an inhibitor of eNOS, in ECIRS1 mice and eNOSKO mice. The mechanism mediating NO's action on PPC differentiation into BAT was identified as the activation of solubilized guanylate cyclase/cGMP protein-dependent kinase Iα/GSK3β (glycogen synthase kinase 3β) pathways. Plasma lipidomics from ECIRS1 mice with NO-induced increased BAT mass revealed elevated 12,13-diHOME production. Infusion of 12,13-diHOME improved endothelial dysfunction and decreased atherosclerosis, whereas its reduction had opposite effects in ApoE-/-mice.
    CONCLUSIONS: Activation of eNOS and endothelial cells by insulin enhanced the differentiation of PPC to BAT and its lipokines and improved systemic bioenergetics and atherosclerosis, suggesting that endothelial dysfunction is a major contributor of energy disequilibrium in obesity.
    Keywords:  atherosclerosis; body weight; cardiovascular disease; fatty acid; obesity
    DOI:  https://doi.org/10.1161/CIRCRESAHA.121.319582
  12. Nat Biotechnol. 2022 May 30.
    Fast and highly sensitive full-length single-cell RNA sequencing using FLASH-seq.
    Vincent Hahaut, Dinko Pavlinic, Walter Carbone, Sven Schuierer, Pierre Balmer, Mathieu Quinodoz, Magdalena Renner, Guglielmo Roma, Cameron S Cowan, Simone Picelli.
      We present FLASH-seq (FS), a full-length single-cell RNA sequencing (scRNA-seq) method with increased sensitivity and reduced hands-on time compared to Smart-seq3. The entire FS protocol can be performed in ~4.5 hours, is simple to automate and can be easily miniaturized to decrease resource consumption. The FS protocol can also use unique molecular identifiers (UMIs) for molecule counting while displaying reduced strand-invasion artifacts. FS will be especially useful for characterizing gene expression at high resolution across multiple samples.
    DOI:  https://doi.org/10.1038/s41587-022-01312-3
  13. Nat Biotechnol. 2022 May 30.
    Scalable single-cell RNA sequencing from full transcripts with Smart-seq3xpress.
    Michael Hagemann-Jensen, Christoph Ziegenhain, Rickard Sandberg.
      Current single-cell RNA sequencing (scRNA-seq) methods with high cellular throughputs sacrifice full-transcript coverage and often sensitivity. Here we describe Smart-seq3xpress, which miniaturizes and streamlines the Smart-seq3 protocol to substantially reduce reagent use and increase cellular throughput. Smart-seq3xpress analysis of peripheral blood mononuclear cells resulted in a granular atlas complete with common and rare cell types. Compared with droplet-based single-cell RNA sequencing that sequences RNA ends, the additional full-transcript coverage revealed cell-type-associated isoform variation.
    DOI:  https://doi.org/10.1038/s41587-022-01311-4
  14. Nucleic Acids Res. 2022 May 26. pii: gkac425. [Epub ahead of print]
    PCGA: a comprehensive web server for phenotype-cell-gene association analysis.
    Chao Xue, Lin Jiang, Miao Zhou, Qihan Long, Ying Chen, Xiangyi Li, Wenjie Peng, Qi Yang, Miaoxin Li.
      Most complex disease-associated loci mapped by genome-wide association studies (GWAS) are located in non-coding regions. It remains elusive which genes the associated loci regulate and in which tissues/cell types the regulation occurs. Here, we present PCGA (https://pmglab.top/pcga), a comprehensive web server for jointly estimating both associated tissues/cell types and susceptibility genes for complex phenotypes by GWAS summary statistics. The web server is built on our published method, DESE, which represents an effective method to mutually estimate driver tissues and genes by integrating GWAS summary statistics and transcriptome data. By collecting and processing extensive bulk and single-cell RNA sequencing datasets, PCGA has included expression profiles of 54 human tissues, 2,214 human cell types and 4,384 mouse cell types, which provide the basis for estimating associated tissues/cell types and genes for complex phenotypes. We develop a framework to sequentially estimate associated tissues and cell types of a complex phenotype according to their hierarchical relationships we curated. Meanwhile, we construct a phenotype-cell-gene association landscape by estimating the associated tissues/cell types and genes of 1,871 public GWASs. The association landscape is generally consistent with biological knowledge and can be searched and browsed at the PCGA website.
    DOI:  https://doi.org/10.1093/nar/gkac425
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